[gmx-users] Tweeking MDP file options to run on GPU

[kala]

Dear friends

                I am trying to run a ternary complex simulation using
gromacs. so far the simulation is time taking on my dual-core maching
36hrs/ns. Fortunately or unfortunately I have a fermi graphics card wherein
I can run the simulation quite fast. Now the unfortunate thing is the
temperature coulpling. I am new to gmx and tweeking the mdp files is out of
my head. I seek for advice for tweeking this mdp file (which i now use for
cpu calculations)  for fast md using mdrun-gpu.

My system

725 Amino acids
2 ligand molecules
1 co-ordinate zn Ion


my MDP-file


title       = Protein-ligand complex NVT equilibration
; Run parameters
integrator  = md        ; leap-frog integrator
nsteps      = 500000    ; 2 * 500000 = 1000 ps (1 ns)
dt          = 0.002     ; 2 fs
; Output control
nstxout     = 0         ; suppress .trr output
nstvout     = 0         ; suppress .trr output
nstenergy   = 1000      ; save energies every 2 ps
nstlog      = 1000      ; update log file every 2 ps
nstxtcout   = 1000      ; write .xtc trajectory every 2 ps
energygrps  = Protein JZ4
; Bond parameters
continuation    = yes           ; first dynamics run
constraint_algorithm = lincs    ; holonomic constraints
constraints     = all-bonds     ; all bonds (even heavy atom-H bonds)
constrained
lincs_iter      = 1             ; accuracy of LINCS
lincs_order     = 4             ; also related to accuracy
; Neighborsearching
ns_type     = grid      ; search neighboring grid cells
nstlist     = 5         ; 10 fs
rlist       = 0.9       ; short-range neighborlist cutoff (in nm)
rcoulomb    = 0.9       ; short-range electrostatic cutoff (in nm)
rvdw        = 1.4       ; short-range van der Waals cutoff (in nm)
; Electrostatics
coulombtype     = PME       ; Particle Mesh Ewald for long-range electrostatics
pme_order       = 4         ; cubic interpolation
fourierspacing  = 0.16      ; grid spacing for FFT
; Temperature coupling is on
tcoupl      = V-rescale                     ; modified Berendsen thermostat
tc-grps     = Protein_JZ4 Water_and_ions    ; two coupling groups -
more accurate
tau_t       = 0.1   0.1                     ; time constant, in ps
ref_t       = 300   300                     ; reference temperature,
one for each group, in K
; Pressure coupling is off
pcoupl      = Parrinello-Rahman             ; pressure coupling is on for NPT
pcoupltype  = isotropic                     ; uniform scaling of box vectors
tau_p       = 2.0                           ; time constant, in ps
ref_p       = 1.0                           ; reference pressure, in bar
compressibility = 4.5e-5                    ; isothermal
compressibility of water, bar^-1
; Periodic boundary conditions
pbc         = xyz       ; 3-D PBC
; Dispersion correction
DispCorr    = EnerPres  ; account for cut-off vdW scheme
; Velocity generation
gen_vel     = yes       ; assign velocities from Maxwell distribution
gen_temp    = 300       ; temperature for Maxwell distribution
gen_seed    = -1        ; generate a random seed

thanks and regards

bharath
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